6F8G: Speckle-type POZ protein

Co-crystal structure of SPOP MATH domain and hamster Pdx1 fragment. Determined by X-ray diffraction at 2.03 Å resolution. Released 28 Nov 2018.

Method: X-ray diffraction
Resolution: 2.03 Å
Organisms: Homo sapiens, Mesocricetus auratus
Chains: 8
Atoms: 5,147
Mol. weight: 71.46 kDa
Released: 28 Nov 2018

Explore 6F8G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6F8G contains 22 α-helices and 47 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	25-38	14	1
β-strand	52-53	2	2
α-helix	54-56	3
β-strand	57-59	3	2
α-helix	61-63	3
β-strand	65-72	8	2
β-strand	73	1	3
β-strand	75	1	3
β-strand	83-92	10	2
β-strand	98-107	10	1
β-strand	113-118	6	1
β-strand	123-125	3	1
β-strand	130-138	9	2
α-helix	139-143	5
α-helix	151-153	3
β-strand	155-163	9	1

Chain B: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	25-38	14	1
α-helix	41-43	3
α-helix	44-48	5
β-strand	52-53	2	4
α-helix	54-56	3
β-strand	57-59	3	4
β-strand	60-61	2	1
β-strand	65-72	8	4
β-strand	83-92	10	4
β-strand	98-107	10	1
β-strand	113-118	6	1
β-strand	123-125	3	1
β-strand	130-138	9	4
α-helix	139-143	5
α-helix	145-147	3
α-helix	151-153	3
β-strand	155-163	9	1

Chain C: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	31-38	8	5
β-strand	52-53	2	6
α-helix	54-56	3
β-strand	57-59	3	6
α-helix	61-63	3
β-strand	65-72	8	6
β-strand	83-92	10	6
β-strand	98-107	10	5
β-strand	113-118	6	5
β-strand	123-125	3	5
β-strand	130-138	9	6
α-helix	139-143	5
α-helix	145-147	3
α-helix	151-153	3
β-strand	155-163	9	5

Chain D: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	31-38	8	7
α-helix	41-43	3
α-helix	44-48	5
β-strand	52-53	2	8
α-helix	54-56	3
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	65-72	8	8
β-strand	83-92	10	8
β-strand	98-107	10	7
β-strand	113-118	6	7
β-strand	123-125	3	7
β-strand	130-138	9	8
α-helix	139-142	4
α-helix	145-147	3
α-helix	151-153	3
β-strand	155-163	9	7

Chain E: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	230-231	2	2

Chains F and G: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	229-230	2	6

Chain H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	230	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Speckle-type POZ protein	A, B, C, D	protein	145	Homo sapiens	O43791 (AlphaFold model)
Pancreas/duodenum homeobox protein 1	E, F, G, H	protein	12	Mesocricetus auratus	P70118 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6F8G_1 Speckle-type POZ protein (chains A, B, C, D)
GAMASGKVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESK
DYLSLYLLLVSCPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDF
LLDEANGLLPDDKLTLFCEVSVVQD

Sequence of entity 2 (E, F, G, H), FASTA

>6F8G_2 Pancreas/duodenum homeobox protein 1 (chains E, F, G, H)
EPEQDSAVTSGE

Primary citation

The Structure of the SPOP-Pdx1 Interface Reveals Insights into the Phosphorylation-Dependent Binding Regulation. Ostertag, M.S., Messias, A.C., Sattler, M. et al. Structure (2019) 27:327-334.e3. DOI 10.1016/j.str.2018.10.005 · PubMed

Other PDB entries of the same protein (UniProt O43791 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3IVV 1.25 Å, Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of…
7LIN 1.44 Å, X-ray structure of SPOP MATH domain (D140G) in complex with a 53BP1 peptide
7D3D 1.45 Å, Crystal structure of SPOP bound with a peptide
9HFV 1.45 Å, MyD88 peptide_2 bound to SPOP MATH domain
7LIP 1.48 Å, X-ray structure of SPOP MATH domain (D140G)
4HS2 1.53 Å, Crystal Structure of the Human SPOP C-terminal Domain
3HQL 1.66 Å, Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of…
3HQM 1.74 Å, Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of…
3IVB 1.75 Å, Structures of SPOP-Substrate Complexes: Insights into Architectures of BTB-Cul3…
6I5P 1.81 Å, Co-crystal structure of human SPOP MATH domain (E47K) and human BRD3 fragment
6I68 1.85 Å, Co-crystal structure of human SPOP MATH domain (M117V) and human BRD3 fragment
6I41 1.9 Å, Co-crystal structure of human SPOP MATH domain (wild-type) and human BRD3 fragment

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